Problems with output file with unclassified sequences

[ayamakawa]

Hi!

I'm having problems when I run the "emu abundance" with the "--output-unclassified". This is the code I used and the resulting error:

emu abundance FL005_16S23S_S01.fasta --db MIrROR_DB/ --output-basename FL005_16S23S_S01.fasta --threads 8 --output-unclassified --keep-files --keep-counts --keep-read-assignments --output-dir 16S23S_results/

[M::mm_idx_gen::6.4841.54] collected minimizers [M::mm_idx_gen::7.0962.02] sorted minimizers [M::main::7.1032.01] loaded/built the index for 97763 target sequence(s) [M::mm_mapopt_update::7.1402.01] mid_occ = 28998 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 97763 [M::mm_idx_stat::7.1642.01] distinct minimizers: 1830421 (44.69% are singletons); average occurrences: 41.694; average spacing: 5.457; total length: 416474652 [M::worker_pipeline::876.2277.93] mapped 7629 sequences [M::worker_pipeline::878.959*7.93] mapped 28 sequences [M::main] Version: 2.26-r1175 [M::main] CMD: minimap2 -ax map-ont -t 8 -N 50 -p .9 -K 500000000 -o 16S23S_results/FL005_16S23S_S01.fasta_emu_alignments.sam MIrROR_DB/species_taxid.fasta FL005_16S23S_m0_S01_noba.fasta FL005_16S23S_m1_S01_noba.fasta [M::main] Real time: 879.049 sec; CPU: 6967.297 sec; Peak RSS: 7.290 GB Unassigned read count: 1 Assigned read count: 7655 Number of EM iterations: 40 Traceback (most recent call last): File "/home/anayamakawa/miniconda3/envs/RESCUE_env/bin/emu", line 829, in output_unclassified(SAM_FILE, "{}_unclassified".format(out_file), INPUT_FILETYPE) File "/home/anayamakawa/miniconda3/envs/RESCUE_env/bin/emu", line 94, in output_unclassified Seq(alignment.query_sequence), File "/home/anayamakawa/miniconda3/envs/RESCUE_env/lib/python3.7/site-packages/Bio/Seq.py", line 1728, in init "data should be a string, bytes, bytearray, Seq, or MutableSeq object" TypeError: data should be a string, bytes, bytearray, Seq, or MutableSeq object

Even with this error, the alignments, assignments distributions and rel abundance files are produced. And if I remove the "--output-unclassified" it works without any error. Would you have any idea what could be the problem?

Thank you!

[kdc10]

Interesting. Could you tell me which version of emu you are running?

[ayamakawa]

I'm using the v3.4.5. I just saw that there's a new version. I will try update and see. I will let you know if worked!

Thank you!

[ayamakawa]

I update and try run again, but the error continues:

emu abundance FL005_16S23S_m?_S01_noba.fasta --db MIrROR_DB/ --output-basename FL005_16S23S_S01.fasta --threads 8 --keep-files --keep-counts --output-unclassified --keep-read-assignments --output-dir 16S23S_results/ [M::mm_idx_gen::6.4601.51] collected minimizers [M::mm_idx_gen::7.1432.03] sorted minimizers [M::main::7.1512.03] loaded/built the index for 97763 target sequence(s) [M::mm_mapopt_update::7.1892.03] mid_occ = 28998 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 97763 [M::mm_idx_stat::7.2112.02] distinct minimizers: 1830421 (44.69% are singletons); average occurrences: 41.694; average spacing: 5.457; total length: 416474652 [M::worker_pipeline::913.9657.93] mapped 7629 sequences [M::worker_pipeline::916.699*7.93] mapped 28 sequences [M::main] Version: 2.26-r1175 [M::main] CMD: minimap2 -ax map-ont -t 8 -N 50 -p .9 -K 500000000 -o 16S23S_results/FL005_16S23S_S01.fasta_emu_alignments.sam MIrROR_DB/species_taxid.fasta FL005_16S23S_m0_S01_noba.fasta FL005_16S23S_m1_S01_noba.fasta [M::main] Real time: 916.800 sec; CPU: 7269.797 sec; Peak RSS: 7.326 GB Unassigned read count: 1 Assigned read count: 7655 Number of EM iterations: 40 Traceback (most recent call last): File "/home/anayamakawa/miniconda3/envs/RESCUE_env/bin/emu", line 839, in output_unclassified(SAM_FILE, "{}_unclassified".format(out_file), INPUT_FILETYPE) File "/home/anayamakawa/miniconda3/envs/RESCUE_env/bin/emu", line 94, in output_unclassified Seq(alignment.query_sequence), File "/home/anayamakawa/miniconda3/envs/RESCUE_env/lib/python3.7/site-packages/Bio/Seq.py", line 1728, in init "data should be a string, bytes, bytearray, Seq, or MutableSeq object" TypeError: data should be a string, bytes, bytearray, Seq, or MutableSeq object

The error continue with other samples and databases. Thank you for the assistance!

[kdc10]

I'm not sure what is causing this and I am unable to reproduce the error. Would you be willing to share your database and your fasta with me? Either here or to email: kristendcurry@gmail.com

[ayamakawa]

Sure! I shared with your e-mail a google drive folder with the files.

Thank you!

[kdc10]

There was a sequence header without a corresponding sequence. Emu has been update to handle this: https://github.com/treangenlab/emu/releases/tag/v3.5.0